Bismark report for: YRVL_R1_001.fastq.gz and YRVL_R2_001.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /Users/yaamini/Documents/project-gigas-oa-meth/analyses/2019-08-30-Bismark-Parameter-Testing/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
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Sequence pairs analysed in total:	10000
Number of paired-end alignments with a unique best hit:	6946
Mapping efficiency:	69.5% 
Sequence pairs with no alignments under any condition:	2336
Sequence pairs did not map uniquely:	718
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3475	((converted) top strand)
GA/CT/CT:	3	(complementary to (converted) top strand)
GA/CT/GA:	7	(complementary to (converted) bottom strand)
CT/GA/GA:	3460	((converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	317202

Total methylated C's in CpG context:	5940
Total methylated C's in CHG context:	2044
Total methylated C's in CHH context:	9978
Total methylated C's in Unknown context:	448


Total unmethylated C's in CpG context:	31832
Total unmethylated C's in CHG context:	49968
Total unmethylated C's in CHH context:	217440
Total unmethylated C's in Unknown context:	2578


C methylated in CpG context:	15.7%
C methylated in CHG context:	3.9%
C methylated in CHH context:	4.4%
C methylated in unknown context (CN or CHN):	14.8%


Bismark completed in 0d 0h 0m 31s